In the episode "Small Potatoes" Gillian Anderson appears to have no pants on for a quick second. Near the end when her and Mulder's imposter are sitting on the couch Mulder bursts in the door and she looks quickly at the imposter and right before she stands up if you pause your VCR real quick you see her knees. Hmm...

I have been pondering this "slip-up" recently, so I just sat down and watched the episode in question. When the imposter posing as Mulder knocks on Scully's door, she is sitting on the floor indian style, with a black pair of slacks on. Nowhere in this entire scene is Scully pantless. From the time "Mulder" enters her apartment until the time when the real Mulder breaks in the door, Scully is wearing black pants. I've watched and rewatched this scene, and the only slip up I have noted is that you have reported information that is incorrect.

It is true that she is not wearing trousers/pants but when her partner/Eddie comes into her apartment,he gives her a bottle of wine and when she goes to open it, you can clearly see that she is wearing a large shirt covering any naughty bits.
She was at home,alone and when she opens the wine she does so by holding it between her legs and getting a corkscrew to complete the job.It was not by any means a blooper or slip-up.